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Resistance to Phytophthora previous termpod rotnext term (Ppr) is becoming an increasingly important criterion for selection of new cocoa cultivars in Côte d'Ivoire. The predominant species of the pathogen, Phytophthora palmivora, causes previous termpodnext term losses of 10-15% but the more aggressive Phytophthora megakarya present in the eastern part of the country causes losses of 40-60%. The latter species is expected to continue its spread to the main cocoa belt in Côte d'Ivoire over the next decade. Since 2000, the Centre National de Recherche Agronomique has been selecting new cocoa cultivars with direct involvement of farmers. More than 250 farmers were visited and their knowledge is being used to collect accessions with high yield potential, with low pest (mirids) infestation or with low Ppr incidence. Farmers were capable of identifying mother trees with low Ppr incidence only in regions with high disease pressure (Abengourou and Aboisso). Open-pollinated seedling progenies obtained from 226 promising trees in farmers¿ fields were screened for resistance to Ppr by inoculating leaf discs from nursery plants with spores of a P. palmivora isolate. Three clones (SCA6, PA150 and NA79) and three recommended hybrids were used as control cultivars. The results of the leaf disc test confirmed the known variation of resistance of the control cultivars. The relative level of resistance of the farm accessions varied mainly between moderately resistant and susceptible, but several accessions could be considered as resistant, in relation to the control cultivars. The major part of the 15% most resistant farm accessions came from the Abengourou and Aboisso regions in the eastern part of the country. Progenies from mother trees that farmers had selected as showing low Ppr incidence in their fields also appeared to be more resistant in the leaf disc test. This suggests that the resistance identified to P. palmivora in the leaf disc test may be efficient in the field in areas infected with P. megakarya. It is recommended that the genetic diversity identified through participatory selection of promising mother trees in farmers¿ fields be further exploited in breeding to obtain new hybrid or clonal cocoa cultivars with low incidence of Ppr, good yield and low mirid damage.

The first linkage map established by Lanaud et al. (1995) was used as a starting point to produce a high-density molecular linkage map. A mapping population of 181 progenies resulting from a cross between two heterozygous genotypes, a Forastero and a Trinitario (hybrid between Forastero and Criollo), was used for the linkage analysis. A new DNA isolation protocol was established, which allows enough good quality DNA to construct a genetic map with PCR-based markers. The map comprises 424 markers with an average spacing between markers of 2.1 cM. The marker types used were five isozymes, six loci from known function genes, 65 genomic RFLPs, 104 cDNA RFLPs, three telomeric probes, 30 RAPDs, 191 AFLPs and 20 microsatellites. The use of new marker types, AFLP and microsatellites, did not disturb the original order of the RFLP loci used on the previous map. The genetic markers were distributed over ten linkage groups and cover 885.4 cM. The maximum distance observed between adjacent markers was 16.2 cM, and 9.4% of all loci showed skewed segregation.

The genetic structure of 175 genotypes of Theobroma cacao L. was investigated using 27 RFLP/cDNA loci. The number of alleles per locus was never higher than four and a high genetic diversity was found. Criollo genotypes appeared differentiated from Forastero genotypes. A deficiency of heterozygotes was found in all populations and some alleles were fixed in some populations. Within population gene diversity was high. When four morphological groups were considered, Upper Amazon Forastero was the most polymorphic and diverse population. Almost all the alleles of the whole species could be found within this group. Observed heterozygosity was the highest within Criollo and Trinitario populations but a certain proportion of homozygous genotypes was present in all groups.

The collection of Cola nitida in Côte d'Ivoire was previously classified, based on isozyme markers, into three groups named A, B and C, based on isozymic differences. In this study, morphological traits and several yield components as well as genotypic and phenotypic variabilities for vigour were investigated in groups A and B. We found that group A was characterized by a low vigour and high yield components. In contrast, group B expressed high vigour and low yield components. Intergroup hybrids were more vigorous and high yielder than intragroup hybrids. The vigour of intergroup hybrids was comparable to that of half sib commercial hybrids. Value of heterosis obtained for the yield of intergroup hybrids was 350%. It was concluded, based on our findings, that reciprocal recurrent selection in Cola nitida using plant materials of groups A and B should lead to significant improvement.

A genetic analysis of resistance of cacao to Phytophthora palmivora was carried out in a 5 × 5 diallel and in a 4 × 2 NC II factorial design, involving cross-progenies and parental clones planted in the nursery and field, respectively. Resistance was scored in the laboratory by inoculation of leaf discs with P. palmivora spores with four replicates and, for the factorial design, results were compared with the percentage of rotten pods in the field assessed over a seven-year period. Significant differences between genotypes were observed for both laboratory and field evaluation methods. For the laboratory test, no reciprocal effect was observed and plant effects within seedling progenies were more significant than plant effects within clones. General combining ability was the main source of variation but specific combining ability was also significant for the leaf disc test applied to the diallel. Heritabilities increased with the number of replicates, reaching values of 0.34 and 0.67 for narrow sense heritability, and 0.60 and 0.67 for broad sense heritability, for the diallel and the factorial design, respectively. These values were higher than observed for the percentage of rotten pods in the field in the factorial design (0.42 and 0.47, respectively). For the leaf test, the expected genetic gains were around 30% with a selection intensity of 5%. The existence of significant genetic (0.71) and phenotypic (0.39) coefficients of correlation between resistance on leaves and percentage of rotten pods in the field in the factorial design confirms the feasibility of using the leaf disc test for early selection of resistance to Phytophthora pod rot of cacao.

Disease resistance and defence gene analog (RGA/DGA) sequences were isolated in cocoa using a PCR approach with degenerate primers designed from conserved domains of plant resistance and defence genes: the NBS (nucleotide binding site) motif present in a number of resistance genes such as the tobacco N, sub-domains of plant serine/threonine kinases such as the Pto tomato gene, and conserved domains of two defence gene families: pathogenesis-related proteins (PR) of classes 2 and 5. Nucleotide identity between thirty six sequences isolated from cocoa and known resistance or defence genes varied from 58 to 80%. Amino acid sequences translated from corresponding coding sequences produced sequences without stop codons, except for one NBS −like sequence. Most of the RGAs could be mapped on the cocoa genome and three clusters of genes could be observed : NBS-like sequences clustered in two regions located on chromosomes 7 and 10, Pto-like sequences mapped in five genome regions of which one, located on chromosome 4, corresponded to a cluster of five different sequences. PR2-like sequences mapped in two regions located on chromosome 5 and 9 respectively. An enrichment of the genetic map with microsatellite markers allowed us to identify several co-localisations of RGAs, DGAs and QTL for resistance to Phytophthora detected in several progenies, particularly on chromosome 4 where a cluster of Pto-like sequences and 4 QTL for resistance to Phytophthora were observed. Many other serious diseases affect cocoa and the candidate genes, isolated in this study, could be of broader interest in cocoa disease management.

A linkage map of cacao based on codominant markers has been constructed by integrating 201 new simple sequence repeats (SSR) developed in this study with a number of isoenzymes, restriction fragment length polymorphisms (RFLP), microsatellite markers and resis- tance and defence gene analogs (Rgenes-RFLP) previ- ously mapped in cacao. A genomic library enriched for (GA)n and (CA)n was constructed, and 201 new mi- crosatellite loci were mapped on 135 individuals from the same mapping population used to establish the first reference maps. This progeny resulted from a cross between two heterozygous cacao clones: an Upper-Ama- zon Forastero (UPA 402) and a Trinitario (UF 676). The new map contains 465 markers (268 SSRs, 176 RFLPs, five isoenzymes and 16 Rgenes-RFLP) arranged in ten linkage groups corresponding to the haploid chromosome number of cacao. Its length is 782.8 cM, with an average interval distance between markers of 1.7 cM. The new microsatellite markers were distributed throughout all linkage groups of the map, but their distribution was not random. The length of the map established with only SSRs was 769.6 cM, representing 94.8% of the total map. The current level of genome coverage is approximately one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across different mapping populations and will allow the identi- fication and comparison of the most important regions involved in the variation of the traits of interest and the development of marker-assisted selection strategies.

La cartographie de locus à caractère quantitatif (QTL) a été réalisée chez le cacaoyer (Theobroma cacao L.) pour des caractères agronomiques. Des régions du génome impliquées dans le rendement, la vigueur et la résistance à Phytophthora palmivora, ont été identifiées. Trois clones hétérozygotes, un Forastero haut Amazonien (IMC78) et deux Trinitario (DR1 et S52) ont été croisés par le même parent mâle (Catongo), Forastero bas Amazonien qui est connu pour être hautement homozygote. Les observations ont été réalisées sur neuf années consécutives. Un à trois QTL impliqués dans le rendement ont été détectés chez chacune des trois populations, localisés sur les chromosomes 1, 2, 4, 5, 9 et 10. Ils ont expliqué entre 8,1 et 19,3% de la variation phénotypique et ont montré différents niveaux de répétabilité. Chez IMC78, le QTL détecté sur le chromosome 5 était le plus stable. Le QTL pour le poids moyen de la cabosse, sur le chromosome 4, était le plus significatif avec un LOD de 17,3 et un R2 de 43,7. Des QTL impliqués dans ces caractères ont été identifiés dans les mêmes régions du génome chez des clones appartenant à différents groupes génétiques. Ceci laisse prévoir que les marqueurs moléculaires pourraient être utilisés pour améliorer les variétés de cacaoyers.

Susceptibility of #Theobroma cacao# L. to mirids (#Distantiella theobromae# Distant and #Sahlbergella singularis# Haglund) was assessed in four seedling progeny trials planted in Cote d'Ivoire by visual estimation of the cumulative damage on a 5 point scale. Although a significant effect of the progenies was identified in all trials, a clear discrimination between entries was only observed in one trial. In three trials, set up according to a North Carolina II design, it was possible to rank the female or the male parents according to the values of their progenies. Genotypes from the upper amazon Forastero appeared to include the most promising parents, while germplasm from the Trinitario (Central America) group appeared as the least promising. A good correlation (R = 0.85) between the phenotypic level of susceptibility of six clones and their general combining ability was observed in one of the trials but not in another trial. Broad and narrow sense heritabilities were identical, varying between 0.09 and 0.38, according to the trial. The highest value was found for the trial comparing genetically diverse parents, represented by a high number of offspring. The prospects of including mirid resistance in cocoa breeding programs are discussed. (Resume d'auteur)

This study aimed to compare the genetic control of cacao resistance to three species of Phytophthora: Phytophthora palmivora, Phytophthora megakarya and Phytophthora capsici. The study was conducted on 151 hybrid progenies created in Cote d'Ivoire and grown in a green-house in Montpellier. Phytophthora resistance was screened by leaf-test inoculation with two different strains per species. Selection of the best individuals for resistance to P. palmivora at a 10% selection rate, would lead to a genetic progress of 47% in the disease evaluation for this species and a genetic progress of 42% and 21% for the two other species. A genetic map with a total length of 682 cM was built with 213 markers, 190 AFLPs and 23 microsatellites. QTLs were identified using composite interval mapping. QTLs were found located in six genomic regions. One of these was detected with five strains belonging to the three Phytophthora species. Two other regions were detected with two or three strains of two different species. Three additional QTLs were detected for only one species of Phytophthora. Each QTL explained between 8 to 12% of the phenotypic variation. For each strain, between 11.5% to 27.5% of the total phenotypic variation could be explained by the QTLs identified. The identification of multiple QTLs involved in resistance to Phytophthora offers the possibility to improve durability of resistance in cocoa by a possible cumulation of many different resistance genes located in different chromosome regions using marker-aided selection.

The genetic diversity of 106 genotypes of #Theobroma cacao# L. was assessed using RFLP and RAPD methods. Thirty-one cDNA probes and 19 primers generated, respectively, 87 and 49 polymorphic bands that were submitted to factorial and cluster analyses. Both RFLP and RAPD bands separated the individuals into three distinctive groups. Some genotypes did not correspond to the currently accepted classification and are considered to have been originally misclassified. The nature of RAPD bands was investigated by Southern analysis. There were as many highly repeated sequences as single copy sequences but the two types of sequences did not structure the variability in the same way. Similar results were obtained with RFLPs and RAPDs with regard to the genetic structure of #Theobioma cacao# L. Therefore, RAPDs appear to be as efficient as RFLPs for classifying cocoa genotypes.